protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17jul05d/protomo_alignments/tiltseries0008_thick200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4087.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2302 --r1_region_y=2226 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4087.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=2226 --r2_region_x=2302 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2044.0 --defocus_ang_positive=90 --r5_mask_width_x=2277 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4087.0 --r3_highpass_apod_x=2044.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=550 --r2_mask_width_y=531 --r5_region_x=2302 --r5_region_y=2226 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=4087.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=2201 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2044.0 --runname=tiltseries0008_thick200 --r1_highpass_diameter_x=4087.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=2277 --r4_mask_width_y=2201 --logging=true --DefocusTol=200 --filter=median --sessionname=17jul05d --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=2044.0 --r1_highpass_apod_x=2044.0 --r2_highpass_apod_x=2044.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=8 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=1088 --r3_mask_width_x=1126 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4087.0 --r4_highpass_diameter_x=4087.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4087.0 --tilt_azimuth=-79.5 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2044.0 --r5_highpass_apod_x=2044.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4087.0 --defocus_max=0 --r4_region_y=2226 --r4_region_x=2302 --r5_kernel_y=5 --r3_region_x=2302 --r3_region_y=2226 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=200 --expid=4317 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=4087.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2044.0 --r4_highpass_apod_y=2044.0 --azimuth=true --r1_mask_width_y=253 --r1_mask_width_x=262 --jobtype=protomo

node20
Start time: 2017yr07m06d-14hr02m53s
Description: 
coarse_series0008_iter2.tlt not found, using coarse_series0008.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0008.tlt to series0008.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.23499008 0.23499008 }
map.sampling = 8
window.highpass.diameter = { 0.00718712013702 0.00718712013702 }
window.highpass.apodization = { 0.0143707240705 0.0143707240705 }
window.mask.apodization = { 10 10 }
align.mask.width = { 262 253 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 18.322267622
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 287 278 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 262 253 }
reference.body = 18.322267622
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0745 for Iteration #1 of Tilt-Series #8.
CCMS(rotations) = 2.74211 for Iteration #1 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8.
The scaled sum of CCMS values is #0.09209 for iteration 1 of Tilt-Series #8.
Alignment quality for Iteration #1 of Tilt-Series #8 (17jul05d): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03691 for Iteration #2 of Tilt-Series #8.
CCMS(rotations) = 1.01626 for Iteration #2 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8.
The scaled sum of CCMS values is #0.03878 for iteration 2 of Tilt-Series #8.
Alignment quality for Iteration #2 of Tilt-Series #8 (17jul05d): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00431 for Iteration #3 of Tilt-Series #8.
CCMS(rotations) = 0.18563 for Iteration #3 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00587 for iteration 3 of Tilt-Series #8.
Alignment quality for Iteration #3 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00392 for Iteration #4 of Tilt-Series #8.
CCMS(rotations) = 0.13136 for Iteration #4 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00459 for iteration 4 of Tilt-Series #8.
Alignment quality for Iteration #4 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #5 of Tilt-Series #8.
CCMS(rotations) = 0.17098 for Iteration #5 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00527 for iteration 5 of Tilt-Series #8.
Alignment quality for Iteration #5 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00374 for Iteration #6 of Tilt-Series #8.
CCMS(rotations) = 0.15893 for Iteration #6 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00505 for iteration 6 of Tilt-Series #8.
Alignment quality for Iteration #6 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #7 of Tilt-Series #8.
CCMS(rotations) = 0.12206 for Iteration #7 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00419 for iteration 7 of Tilt-Series #8.
Alignment quality for Iteration #7 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00432 for Iteration #8 of Tilt-Series #8.
CCMS(rotations) = 0.18711 for Iteration #8 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0059 for iteration 8 of Tilt-Series #8.
Alignment quality for Iteration #8 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #9 of Tilt-Series #8.
CCMS(rotations) = 0.12616 for Iteration #9 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00435 for iteration 9 of Tilt-Series #8.
Alignment quality for Iteration #9 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00392 for Iteration #10 of Tilt-Series #8.
CCMS(rotations) = 0.17665 for Iteration #10 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00549 for iteration 10 of Tilt-Series #8.
Alignment quality for Iteration #10 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.233125079365 0.233125079365 }
map.sampling = 4
window.highpass.diameter = { 0.00359356006851 0.00359356006851 }
window.highpass.apodization = { 0.00718536203523 0.00718536203523 }
window.mask.apodization = { 10 10 }
align.mask.width = { 550 531 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 36.6445352439
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 575 556 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 550 531 }
reference.body = 36.6445352439
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00468 for Iteration #11 of Tilt-Series #8.
CCMS(rotations) = 0.10479 for Iteration #11 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00444 for iteration 11 of Tilt-Series #8.
Alignment quality for Iteration #11 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #8 (17jul05d): UnstableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00396 for Iteration #12 of Tilt-Series #8.
CCMS(rotations) = 0.13194 for Iteration #12 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00462 for iteration 12 of Tilt-Series #8.
Alignment quality for Iteration #12 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #13 of Tilt-Series #8.
CCMS(rotations) = 0.11938 for Iteration #13 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00443 for iteration 13 of Tilt-Series #8.
Alignment quality for Iteration #13 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #14 of Tilt-Series #8.
CCMS(rotations) = 0.12509 for Iteration #14 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00448 for iteration 14 of Tilt-Series #8.
Alignment quality for Iteration #14 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #15 of Tilt-Series #8.
CCMS(rotations) = 0.11789 for Iteration #15 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00432 for iteration 15 of Tilt-Series #8.
Alignment quality for Iteration #15 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #16 of Tilt-Series #8.
CCMS(rotations) = 0.13377 for Iteration #16 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00465 for iteration 16 of Tilt-Series #8.
Alignment quality for Iteration #16 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #17 of Tilt-Series #8.
CCMS(rotations) = 0.12094 for Iteration #17 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00435 for iteration 17 of Tilt-Series #8.
Alignment quality for Iteration #17 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #18 of Tilt-Series #8.
CCMS(rotations) = 0.12785 for Iteration #18 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00447 for iteration 18 of Tilt-Series #8.
Alignment quality for Iteration #18 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #19 of Tilt-Series #8.
CCMS(rotations) = 0.11714 for Iteration #19 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00416 for iteration 19 of Tilt-Series #8.
Alignment quality for Iteration #19 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #20 of Tilt-Series #8.
CCMS(rotations) = 0.13237 for Iteration #20 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00462 for iteration 20 of Tilt-Series #8.
Alignment quality for Iteration #20 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #3 of Tilt-Series #8 (tiltseries0008_thick200)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.23688516129 0.23688516129 }
map.sampling = 2
window.highpass.diameter = { 0.00179678003425 0.00179678003425 }
window.highpass.apodization = { 0.00359268101761 0.00359268101761 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1126 1088 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 73.2890704878
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1151 1113 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1126 1088 }
reference.body = 73.2890704878
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00344 for Iteration #21 of Tilt-Series #8.
CCMS(rotations) = 0.11306 for Iteration #21 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00398 for iteration 21 of Tilt-Series #8.
Alignment quality for Iteration #21 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #8 (17jul05d): Very StableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00375 for Iteration #22 of Tilt-Series #8.
CCMS(rotations) = 0.08849 for Iteration #22 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00365 for iteration 22 of Tilt-Series #8.
Alignment quality for Iteration #22 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00346 for Iteration #23 of Tilt-Series #8.
CCMS(rotations) = 0.10082 for Iteration #23 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00375 for iteration 23 of Tilt-Series #8.
Alignment quality for Iteration #23 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00335 for Iteration #24 of Tilt-Series #8.
CCMS(rotations) = 0.08119 for Iteration #24 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0033 for iteration 24 of Tilt-Series #8.
Alignment quality for Iteration #24 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0035 for Iteration #25 of Tilt-Series #8.
CCMS(rotations) = 0.09281 for Iteration #25 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0036 for iteration 25 of Tilt-Series #8.
Alignment quality for Iteration #25 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.2294825 0.2294825 }
map.sampling = 1
window.highpass.diameter = { 0.000898390017127 0.000898390017127 }
window.highpass.apodization = { 0.00179634050881 0.00179634050881 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2277 2201 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 146.578140976
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2302 2226 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2277 2201 }
reference.body = 146.578140976
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00459 for Iteration #26 of Tilt-Series #8.
CCMS(rotations) = 0.13009 for Iteration #26 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00489 for iteration 26 of Tilt-Series #8.
Alignment quality for Iteration #26 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00396 for Iteration #27 of Tilt-Series #8.
CCMS(rotations) = 0.137 for Iteration #27 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00472 for iteration 27 of Tilt-Series #8.
Alignment quality for Iteration #27 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00513 for Iteration #28 of Tilt-Series #8.
CCMS(rotations) = 0.12232 for Iteration #28 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00501 for iteration 28 of Tilt-Series #8.
Alignment quality for Iteration #28 of Tilt-Series #8 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00478 for Iteration #29 of Tilt-Series #8.
CCMS(rotations) = 0.10722 for Iteration #29 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00453 for iteration 29 of Tilt-Series #8.
Alignment quality for Iteration #29 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00555 for Iteration #30 of Tilt-Series #8.
CCMS(rotations) = 0.108 for Iteration #30 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00493 for iteration 30 of Tilt-Series #8.
Alignment quality for Iteration #30 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00498 for Iteration #31 of Tilt-Series #8.
CCMS(rotations) = 0.11052 for Iteration #31 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0047 for iteration 31 of Tilt-Series #8.
Alignment quality for Iteration #31 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00356 for Iteration #32 of Tilt-Series #8.
CCMS(rotations) = 0.11098 for Iteration #32 of Tilt-Series #8.
CCMS(scale) = 0.00217 for Iteration #32 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00339 for iteration 32 of Tilt-Series #8.
Alignment quality for Iteration #32 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00422 for Iteration #33 of Tilt-Series #8.
CCMS(rotations) = 0.13011 for Iteration #33 of Tilt-Series #8.
CCMS(scale) = 0.00265 for Iteration #33 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00403 for iteration 33 of Tilt-Series #8.
Alignment quality for Iteration #33 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #8 (17jul05d): StableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00414 for Iteration #34 of Tilt-Series #8.
CCMS(rotations) = 0.10399 for Iteration #34 of Tilt-Series #8.
CCMS(scale) = 0.00269 for Iteration #34 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00366 for iteration 34 of Tilt-Series #8.
Alignment quality for Iteration #34 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #8 (17jul05d): Very StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #8 (tiltseries0008_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #8 (tiltseries0008_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00375 for Iteration #35 of Tilt-Series #8.
CCMS(rotations) = 0.10329 for Iteration #35 of Tilt-Series #8.
CCMS(scale) = 0.00263 for Iteration #35 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0035 for iteration 35 of Tilt-Series #8.
Alignment quality for Iteration #35 of Tilt-Series #8 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #8 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #8 (tiltseries0008_thick200)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr07m07d-01hr04m51s